To pick the peaks in a particular area, hold down Shift and Ctrl (Cmd on a Mac) while left-dragging the mouse. A blue box will be drawn and peaks will be picked at all visible extrema (maxima and minima) in that area. If you find you are picking too many or too few peaks, adjust your contour levels and remember to show/hide positive/negative contours depending on which you would like to have picked. For more information on adjusting contour levels, go to Customise Spectrum Display.
Alternatively you can type PP or go to Spectrum / Pick Peaks / Pick ND Peaks.... A pop-up will appear in which you can select the area in which you would like to pick peaks (by default the whole spectrum area is included). Choose whether to pick positive or negative peaks or both and click on Find Peaks to pick your peaks.
Press Shift and Ctrl/Cmd while left-clicking the mouse where you would like to place your peak.
Alternatively you can type MM and the mouse will go into peak picking mode. You can now easily place multiple peaks in various places in quick succession. Type MM again to exit the peak picking mouse mode.
If you would like to snap any manually placed peaks to their closest extrama (maximum or minimum), simply select them and type SE.
This is the same as peak picking in 2D spectra, but be aware that if you are not in the plane containing the maximum or minimum of your peak, Shift + Ctrl/Cmd + left-dragging to pick a peak may not work. Move planes until you think you are near the maximum and try again, or place a peak maually and type SE. Navigate to the correct plane to find the peak on the peak extremum.
It is also possible to peak pick a 3D spectrum based on its 2D root spectrum. This will be described elsewhere.
In the Project Preferences (go to Project / Preferences or type Ctrl/Cmd + ,) in the Spectrum tab you will find the Peak Picking Drop parameter. This is the percentage by which a peak must drop off from its maximum in all directions (or rise from its minimum) in order to be recognised as a peak. The higher this value, the less likely you are to pick partially overlapped peaks or peaks with shoulders on them.